BMW's OEM ipod solution uses a cable and electronics box connected to the CD changer inputs on the head unit - installation involves rearranging some of the connector pins on the existing head unit plug as well. The normal install involves drilling a hole in the side of the glovebox for the ipod cable to come through, so it sounds likely that is what you have.
If you or someone you know has an ipod/iphone, plug it in and switch the head unit to the CDC input to see if works.
As for the AUX input, that's a different set of pins on the head unit. If you have a 2007 or newer car, it should already have an AUX input on the panel under the climate controls. If not it's a fairly easy 'add on', but you need to take out the radio to access the connector.